{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0877CWMW/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0877CWMW",
"aliases": [
"bradley-bernstein:scRNA Lib 74",
"buenrostro-bernstein:scRNA Lib 74"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002631/",
"assay_slims": [
"gene expression"
],
"status": "released",
"term_name": "single-cell RNA sequencing assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0877CWMW](/measurement-sets/IGVFDS0877CWMW/) has in progress subobject tabular file [IGVFFI0400MBIM](/tabular-files/IGVFFI0400MBIM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0877CWMW/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM8719IQYM](/tissues/IGVFSM8719IQYM/) is missing `upper_bound_age`, `lower_bound_age`, and `age_units`. Tissues, primary cells, and whole organisms are expected to specify a lower bound age, upper bound age, and age units.",
"level": 40,
"level_name": "WARNING",
"name": "audit_biosample_age",
"path": "/tissues/IGVFSM8719IQYM/"
}
]
},
"award": {
"@id": "/awards/HG011986/",
"component": "mapping",
"contact_pi": {
"@id": "/users/33c6eb70-e143-4f77-9661-4b3905737daa/",
"title": "Jason Buenrostro"
},
"title": "A foundational resource of functional elements, TF footprints and gene regulatory interactions"
},
"control_for": [],
"creation_timestamp": "2023-08-28T17:58:19.584023+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO1318PLKS/",
"accession": "IGVFDO1318PLKS",
"aliases": [
"bradley-bernstein:Donor 1503",
"buenrostro-bernstein:Donor 1503"
],
"sex": "female",
"status": "released",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI0633GTTI/",
"accession": "IGVFFI0633GTTI",
"aliases": [
"bradley-bernstein:SS-LS_1983_R1",
"bradley-bernstein:SS-LS_61_R1",
"buenrostro-bernstein:SS-LS_1983_R1",
"buenrostro-bernstein:SS-LS_61_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T18:21:08.299231+00:00",
"file_format": "fastq",
"file_size": 404881060,
"href": "/sequence-files/IGVFFI0633GTTI/@@download/IGVFFI0633GTTI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/08/28/04533ef1-60b9-4ded-be73-8ef4a4da4f31/IGVFFI0633GTTI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-136_L1_SS-PKR-130_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8354RXRJ/",
"accession": "IGVFFI8354RXRJ",
"aliases": [
"bradley-bernstein:SS-LS_1983_R2",
"bradley-bernstein:SS-LS_61_R2",
"buenrostro-bernstein:SS-LS_1983_R2",
"buenrostro-bernstein:SS-LS_61_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T18:21:09.150695+00:00",
"file_format": "fastq",
"file_size": 709458622,
"href": "/sequence-files/IGVFFI8354RXRJ/@@download/IGVFFI8354RXRJ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/08/28/bc9ec91c-369e-48d1-9edd-e3fe2c26104f/IGVFFI8354RXRJ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-136_L1_SS-PKR-130_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5669BPLY/",
"accession": "IGVFFI5669BPLY",
"aliases": [
"bradley-bernstein:SS-LS_2011_R1",
"bradley-bernstein:SS-LS_245_R1",
"buenrostro-bernstein:SS-LS_2011_R1",
"buenrostro-bernstein:SS-LS_245_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T18:21:12.338339+00:00",
"file_format": "fastq",
"file_size": 405003993,
"href": "/sequence-files/IGVFFI5669BPLY/@@download/IGVFFI5669BPLY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/08/28/575f9e1f-b7eb-4e98-a9c0-0b2a7a512768/IGVFFI5669BPLY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-136_L2_SS-PKR-130_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8558RDPT/",
"accession": "IGVFFI8558RDPT",
"aliases": [
"bradley-bernstein:SS-LS_2011_R2",
"bradley-bernstein:SS-LS_245_R2",
"buenrostro-bernstein:SS-LS_2011_R2",
"buenrostro-bernstein:SS-LS_245_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T18:21:13.314392+00:00",
"file_format": "fastq",
"file_size": 710797652,
"href": "/sequence-files/IGVFFI8558RDPT/@@download/IGVFFI8558RDPT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/08/28/1baa80ab-377b-4699-aeee-d22f8e4d6e49/IGVFFI8558RDPT.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-136_L2_SS-PKR-130_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5867RRUA/",
"accession": "IGVFFI5867RRUA",
"aliases": [
"buenrostro-bernstein:SS-LS_1983_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:50:46.421070+00:00",
"file_format": "yaml",
"file_size": 1228,
"href": "/configuration-files/IGVFFI5867RRUA/@@download/IGVFFI5867RRUA.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/17/f49cb2e9-e0b8-41bf-9ca2-4dfa170c2284/IGVFFI5867RRUA.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_1983_seqspecv3.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2318ANJC/",
"accession": "IGVFFI2318ANJC",
"aliases": [
"buenrostro-bernstein:SS-LS_2011_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:50:39.857289+00:00",
"file_format": "yaml",
"file_size": 1229,
"href": "/configuration-files/IGVFFI2318ANJC/@@download/IGVFFI2318ANJC.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/17/2fac6d87-51cc-4b4c-b9be-a097616dcc3a/IGVFFI2318ANJC.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_2011_seqspecv3.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS0635KHHW/"
],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"multiome_size": 6,
"notes": "Preferred_assay_titles enum SHARE-Seq has been renamed to be SHARE-seq.",
"onlist_files": [
"/tabular-files/IGVFFI0400MBIM/"
],
"onlist_method": "multi",
"preferred_assay_title": "SHARE-seq",
"protocols": [
"https://www.protocols.io/view/share-seq-protocol-v2-2-di3y4gpw"
],
"related_multiome_datasets": [
{
"@id": "/measurement-sets/IGVFDS3032KHHX/",
"accession": "IGVFDS3032KHHX",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8556WPGM/",
"accession": "IGVFDS8556WPGM",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS9693BTRP/",
"accession": "IGVFDS9693BTRP",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4704VICJ/",
"accession": "IGVFDS4704VICJ",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6361NSJR/",
"accession": "IGVFDS6361NSJR",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:18:37.653666+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM8719IQYM/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8719IQYM",
"aliases": [
"bradley-bernstein:BioSam 4561_SS-PKR 130",
"buenrostro-bernstein:BioSam 4561_SS-PKR 130"
],
"cellular_sub_pool": "SS-PKR 130",
"classifications": [
"tissue"
],
"institutional_certificates": [],
"sample_terms": [
{
"@id": "/sample-terms/UBERON_0000955/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "brain",
"term_name": "brain"
}
],
"status": "released",
"summary": "Mus musculus C57BL/6 (female) brain tissue (cellular sub pool: SS-PKR 130)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2023-08-28T18:21:08.299231+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "704de206-e4d2-49ba-b666-0edcfa31a9a9"
}